Locus 4635

Sequence ID X_DroMel_CAF1
Location 12,111,865 – 12,111,997
Length 132
Max. P 0.907942
window7616 window7617 window7618

overview

Window 6

Location 12,111,865 – 12,111,957
Length 92
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 76.22
Mean single sequence MFE -26.62
Consensus MFE -9.85
Energy contribution -10.80
Covariance contribution 0.95
Combinations/Pair 1.09
Mean z-score -2.62
Structure conservation index 0.37
SVM decision value 1.06
SVM RNA-class probability 0.907942
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12111865 92 + 22224390
-----------GGCAAAAACUUUGCACAUUAAAAUAUGUAAAUUUUAAUUUGAAACAAAAGGGUUGACGGUUGGCA--------GGCAG-UCAG--------CCCUCGCCAACCGUUGAC
-----------........((((.((.((((((((......)))))))).)).....)))).((..(((((((((.--------(((..-...)--------))...)))))))))..)) ( -30.60)
>DroGri_CAF1 66181 94 + 1
GAAGAGCGCUUCGC-AAAACUUUGCACAUUAAAAUAUGUAAAUUUUAAUUUGAAACAAAAGGGUUGACGUGCUGCU--------GCCAACUCCC--------CCCUUACCG---------
....(((((..(((-((..((((.((.((((((((......)))))))).)).....))))..))).)).)).)))--------..........--------.........--------- ( -17.00)
>DroSec_CAF1 24013 91 + 1
-----------GGCAAAAACUUUGCACAUUAAAAUAUGUAAAUUUUAAUUUGAAACAAAAGGGUUGACGGUUGGCA--------GGCAG-UCAG--------C-CUCGCCAACCGUUGAC
-----------........((((.((.((((((((......)))))))).)).....)))).((..((((((((((--------(((..-...)--------)-)).)))))))))..)) ( -33.70)
>DroYak_CAF1 36871 92 + 1
-----------GGCAAAAACUUUGCACAUUAAAAUAUGUAAAUUUUAAUUUGAAACAAAAGGGUUGACGGUUGGCA--------GGCAG-UCAG--------CCCUCGCCAAACGUUGAC
-----------(((..........((.((((((((......)))))))).)).......(((((((((.(((....--------))).)-))))--------)))).))).......... ( -25.90)
>DroAna_CAF1 3422 108 + 1
-----------GGCAGAAAGUUUGCACAUUAAAAUAUGUAAAUUUUAAUUUGAAACAAAAGGGUUGACGGCUGGCAGGACGGCAGGCAG-UCAGGCAGCCCUUCCUCGCCAAAUGUUGAC
-----------(((.....((((.((.((((((((......)))))))).))))))..((((((((..(((((.(.........).)))-))...))))))))....))).......... ( -31.80)
>DroPer_CAF1 49648 90 + 1
GA--AGCGUUCGGCAAAAACUUUGCACAUUAAAAUAUGUAAAUUUUAAUUUGAAACAAAAGGGUUGACG--UGGCA--------G------------------CCCCGCCAACCGUUGAC
..--((((...(((..........((.((((((((......)))))))).))........((((((...--...))--------)------------------))).)))...))))... ( -20.70)
>consensus
___________GGCAAAAACUUUGCACAUUAAAAUAUGUAAAUUUUAAUUUGAAACAAAAGGGUUGACGGUUGGCA________GGCAG_UCAG________CCCUCGCCAACCGUUGAC
...................((((.((.((((((((......)))))))).)).....)))).((..(((..((((................................))))..)))..)) ( -9.85 = -10.80 +   0.95)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 12,111,865 – 12,111,957
Length 92
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 76.22
Mean single sequence MFE -26.08
Consensus MFE -9.14
Energy contribution -10.31
Covariance contribution 1.17
Combinations/Pair 1.12
Mean z-score -2.48
Structure conservation index 0.35
SVM decision value 0.58
SVM RNA-class probability 0.788325
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12111865 92 - 22224390
GUCAACGGUUGGCGAGGG--------CUGA-CUGCC--------UGCCAACCGUCAACCCUUUUGUUUCAAAUUAAAAUUUACAUAUUUUAAUGUGCAAAGUUUUUGCC-----------
((..(((((((((..(((--------(...-..)))--------))))))))))..))..((((((.....((((((((......))))))))..))))))........----------- ( -29.20)
>DroGri_CAF1 66181 94 - 1
---------CGGUAAGGG--------GGGAGUUGGC--------AGCAGCACGUCAACCCUUUUGUUUCAAAUUAAAAUUUACAUAUUUUAAUGUGCAAAGUUUU-GCGAAGCGCUCUUC
---------....(((((--------(((.((((((--------........)))))))))...(((((..((((((((......))))))))..((((....))-))))))).))))). ( -24.60)
>DroSec_CAF1 24013 91 - 1
GUCAACGGUUGGCGAG-G--------CUGA-CUGCC--------UGCCAACCGUCAACCCUUUUGUUUCAAAUUAAAAUUUACAUAUUUUAAUGUGCAAAGUUUUUGCC-----------
((..(((((((((.((-(--------(...-..)))--------))))))))))..))..((((((.....((((((((......))))))))..))))))........----------- ( -30.80)
>DroYak_CAF1 36871 92 - 1
GUCAACGUUUGGCGAGGG--------CUGA-CUGCC--------UGCCAACCGUCAACCCUUUUGUUUCAAAUUAAAAUUUACAUAUUUUAAUGUGCAAAGUUUUUGCC-----------
((..(((.(((((..(((--------(...-..)))--------)))))).)))..))..((((((.....((((((((......))))))))..))))))........----------- ( -22.60)
>DroAna_CAF1 3422 108 - 1
GUCAACAUUUGGCGAGGAAGGGCUGCCUGA-CUGCCUGCCGUCCUGCCAGCCGUCAACCCUUUUGUUUCAAAUUAAAAUUUACAUAUUUUAAUGUGCAAACUUUCUGCC-----------
..........(((.(((((((((((.(.((-(.(....).)))..).))))).........(((((.....((((((((......))))))))..))))))))))))))----------- ( -27.80)
>DroPer_CAF1 49648 90 - 1
GUCAACGGUUGGCGGGG------------------C--------UGCCA--CGUCAACCCUUUUGUUUCAAAUUAAAAUUUACAUAUUUUAAUGUGCAAAGUUUUUGCCGAACGCU--UC
......((((((((((.------------------.--------..)).--))))))))..(((((.....((((((((......))))))))..)))))((((.....))))...--.. ( -21.50)
>consensus
GUCAACGGUUGGCGAGGG________CUGA_CUGCC________UGCCAACCGUCAACCCUUUUGUUUCAAAUUAAAAUUUACAUAUUUUAAUGUGCAAAGUUUUUGCC___________
((..(((.((((((..............................)))))).)))..))...(((((.....((((((((......))))))))..))))).................... ( -9.14 = -10.31 +   1.17)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 12,111,894 – 12,111,997
Length 103
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 85.57
Mean single sequence MFE -38.18
Consensus MFE -25.46
Energy contribution -26.18
Covariance contribution 0.72
Combinations/Pair 1.09
Mean z-score -3.11
Structure conservation index 0.67
SVM decision value 0.05
SVM RNA-class probability 0.559742
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12111894 103 + 22224390
AAUUUUAAUUUGAAACAAAAGGGUUGACGGUUGGCA--------GGCAGUCAG--------CCCUCGCCAACCGUUGACGGCAAUGGCGACGAUGACGACGCCUCCUCAGCCACCUUUA
.................(((((((..(((((((((.--------(((.....)--------))...)))))))))..))(((...((((.((....)).))))......))).))))). ( -43.10)
>DroSec_CAF1 24042 102 + 1
AAUUUUAAUUUGAAACAAAAGGGUUGACGGUUGGCA--------GGCAGUCAG--------C-CUCGCCAACCGUUGACGGCAAUGGCGACGAUGACGACGCCUCCUCAGCCACCUUAA
..................((((((..((((((((((--------(((.....)--------)-)).)))))))))..))(((...((((.((....)).))))......))).)))).. ( -45.30)
>DroEre_CAF1 35564 103 + 1
AAUUUUAAUUUGAAACAAAAGGGUUGACGGUUGGCA--------GGCAGUCAG--------CCCUCGCCAACCGUUGACGGCAAUGGCGACGAUGACGACGCCUCCUCAGCCACCUUAA
..................((((((..(((((((((.--------(((.....)--------))...)))))))))..))(((...((((.((....)).))))......))).)))).. ( -42.20)
>DroYak_CAF1 36900 103 + 1
AAUUUUAAUUUGAAACAAAAGGGUUGACGGUUGGCA--------GGCAGUCAG--------CCCUCGCCAAACGUUGACGGCAAUGGCGACGAUGACGACGCUUCCUCAGCCACCUUAA
..................((((((..(((.(((((.--------(((.....)--------))...))))).)))..))(((...((((.((....)).))))......))).)))).. ( -33.70)
>DroAna_CAF1 3451 115 + 1
AAUUUUAAUUUGAAACAAAAGGGUUGACGGCUGGCAGGACGGCAGGCAGUCAGGCAGCCCUUCCUCGCCAAAUGUUGACGGCAAUGGCGACGAUGACGACGCC---UCAACCACCUUU-
.................(((((((..(((..((((((((.(((..((......)).)))..)))).))))..)))..))((....((((.((....)).))))---....)).)))))- ( -39.50)
>DroPer_CAF1 49686 86 + 1
AAUUUUAAUUUGAAACAAAAGGGUUGACG--UGGCA--------G-----------------CCCCGCCAACCGUUGACGGCAAUGGCGACGAUGACGACGCCU---CAACCACCG---
....................((((..(((--((((.--------.-----------------....))))..)))..))((....((((.((....)).)))).---...)).)).--- ( -25.30)
>consensus
AAUUUUAAUUUGAAACAAAAGGGUUGACGGUUGGCA________GGCAGUCAG________CCCUCGCCAACCGUUGACGGCAAUGGCGACGAUGACGACGCCUCCUCAGCCACCUUAA
..................((((((..(((.(((((...............................))))).)))..))(((...((((.((....)).))))......))).)))).. (-25.46 = -26.18 +   0.72)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:29:54 2006